Package csb :: Package bio :: Package io :: Module wwpdb :: Class RobustResidueMapper

Class RobustResidueMapper

           object --+    
                    |    
AbstractResidueMapper --+
                        |
                       RobustResidueMapper

Exhaustive residue mapper, which uses Needleman-Wunsch global alignment. Much slower (quadratic), but fail-proof even with incompatible sequences (can insert gaps in both the sparse and the reference sequence).

Nested Classes
	GlobalAligner
Inherited from `AbstractResidueMapper`: `__metaclass__`

Instance Methods

__init__(self, match=1, mismatch=-10, gap=0)
x.__init__(...) initializes x; see help(type(x)) for signature

source code

SparseChainSequence

map(self, sparse, reference)
Map sparse's residues to reference. source code

Inherited from AbstractResidueMapper: create_gap

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Class Variables
	__abstractmethods__ = `frozenset([])`

Properties
Inherited from `object`: `__class__`

Method Details

init(self, match=1, mismatch=-10, gap=0)
(Constructor)

source code

x.__init__(...) initializes x; see help(type(x)) for signature

Parameters:

match (float) - score for a match
mismatch (float) - score for a mismatch (by default mismatches are heavily penalized, while gaps are allowed)
gap (float) - gap penalty

Overrides: object.__init__

(inherited documentation)

map(self, sparse, reference)

source code

Map sparse's residues to reference. Return all sparse residues, aligned over reference, with artificial gap residues inserted at relevant positions. The resulting sequence of sparse residues will always have the same length as the reference sequence.

Parameters:

sparse - sparse sequence (e.g. derived from ATOMS records)
reference - reference, complete sequence (e.g. derived from SEQRES records)

Returns: SparseChainSequence

all sparse residues, optimally aligned over reference (with gaps)

Raises:

ResidueMappingError - if the specified sequences are not alignable

Overrides: AbstractResidueMapper.map

(inherited documentation)

Class RobustResidueMapper

__init__(self, match=1, mismatch=-10, gap=0) (Constructor)

map(self, sparse, reference)

init(self, match=1, mismatch=-10, gap=0)
(Constructor)